Birth defects are among the leading causes of infant mortality worldwide, yet primary prevention is limited. Congenital heart defects, including right- and left-sided obstructive heart defects (OHDs), are among the most serious and lethal of birth defects. Congenital heart defects occur in 8 of every 1,000 live births in the United States, and a quarter of these are OHDs. Most genetic studies of OHDs have focused on specific biological pathways, leaving the vast majority of the genome unexplored. We propose, therefore, a genome-wide scan of OHDs, taking advantage of recently available genetic tools based on the International HapMap and 1000 Genomes projects. We hypothesize that OHDs are associated with maternal and infant genetic variants, copy number variants (CNVs), and gene-specific DNA methylation patterns. Crucial to the proposed study is our access to thousands of previously collected DNA samples from the National Birth Defects Prevention Study (NBDPS). The NBDPS is the largest case-control study of birth defects ever conducted in the United States. Its sample is a well-characterized population-based cohort defined by uniform diagnostic criteria, which has accompanying maternal reports of pregnancy exposures and lifestyle factors. In the discovery phase of our proposed project, we will use the Illumina HumanOmni2.5-8 BeadChip to genotype both common and rare single nucleotide polymorphisms (SNPs) and CNVs in 1,000 case-parental triads and control-maternal dyads (5,000 subjects total) who participated in the Arkansas, California, or Iowa NBDPS sites. In the validation phase, we will use a custom GoldenGate SNP array to validate the role of 1,536 SNPs identified in the discovery phase, in a sample of 1,000 case-parental triads and 1,000 control-maternal dyads (again, 5,000 subjects total) who participated in the five remaining NBDPS sites. In parallel to these efforts, we will compare gene-specific methylation profiles between 250 OHD case-maternal dyads to those of 250 control-maternal dyads (1,000 subjects total) using the Illumina Infinium HumanMethylation450 BeadChip. Our project brings together expert scientists from six birth defects research programs to integrate genomic and epigenomic findings and identify novel pathways involved in the etiology of OHDs. Through our discoveries, we will contribute to a substantially richer understanding of the etiology of OHDs, providing a foundation for public health and clinical prevention and treatment strategies.